One possible ending to stories in which the hero or heroes are trapped in an Alternate Universe is to somehow force the universes to merge or collapse into one single time-line that exhibits (hopefully the best) features of both. A way to Save Both Worlds, if you will.

The current world is headed to nothing short of disaster, so the only choice is to put it back a different way.

Examples:

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Anime & Manga

In the manga Mugen Densetsu Takamagahara: Dream Saga, awakening Amaterasu is meant to restore both worlds to their original, unpolluted glory. However, the ending offers the idea that Making a Better World isn't always better: the team learns that the original two worlds have to be destroyed and their populations killed. They resolve to Save Both Worlds instead of make new ones.

The objective of the villain in Noein is to converge the infinite possible universes into one world, which he thinks would be free from suffering. It also comes at the cost of all individuality ceasing to exist.

In 11eyes, Kakeru comes to the realization late in the game that every one of the chosen ones was drawn from another, slightly different, reality since memories and information don't match up. Everyone worries that they have to die because of Liselotte's soul in them and when the battle is finished, they won't be able to see each other again. Kukuri heals the world back to normal. Everyone ends up staying together in the same world, a composite of all of theirs. They'd become such a tight group of True Companions that it would be too cruel to split them apart.

Used mildly in the Shara/Shuraarc of Tsubasa Reservoir Chronicle. In this case, the main characters don't even realize they are time traveling, but their actions do result in friendlier interactions in the original world. Not that there aren't consequences....

Inverted in Super Dimension Century Orguss. The protagonist's actions have caused a Merged Reality, it's wreaking havoc, and it becomes his and others' job to undo the damage and split all the realities and timelines back up.

Subverted like mad with The DCU character Superboy-Prime. His motivation is that he wants to bring back his world, the "perfect" world... and he's willing to blow up every other world in existence to do it. Moreover, he has no problem killing anyone who gets in his way (or anyone who doesn't), because he judges them to be "stupid" versions of people who'd exist on his world. Yes, to some extent, he is a superpowered avatar of fanboy rage.

The DC and Marvel multiverses briefly merge together into the Amalgam Universe in DC vs Marvel. Years later they are merged again (but not creating the Amalgam universe) in the JLA-Avengers crossover.

Happens with the DC, Wildstorm and (sorta) Vertigo universes at the end of Flashpoint. After the Flash is revealed to have accidentally broken the timeline, leading to events in Flashpoint, Pandora merges the three universes together to fix the problem. (why she can't simply undo the damage and has to merge in the other universes is not explained) This leads directly to the DC reboot and the New52, with some Wildstorm and Vertigo characters and concepts being added to the DCU.

The 2015 Secret Wars is more or less Marvel's version of Crisis on Infinite Earths, and it's been revealed that it will culminate in the merger of every single dimension in the Marvel Multiverse into an All-New Marvel, the most prominent being Earth-616 (Mainstream Marvel) and Earth-1610 (Ultimate Marvel).

Literature

Piers Anthony's Apprentice Adept series eventually merges the two worlds into one; as the characters are explicitly paired across both worlds (mirror-universe twin kinda thing), each pair merges into one being, and each pair has to time-share their body. Substantially easier for the heroes than for the villains, since heroes are used to putting the needs of others on par with or ahead of their own.

Diana Wynne Jones's book Witch Week ends this way, with the merging character explaining to the cast that they will all melt quietly into the people they really are in the other world. Since they're probably going to be burned as witches otherwise, this sounds quite appealing. ('Probably' in context means 'if the world isn't destroyed first,' which is what will happen if their world (which was not supposed to exist) isn't merged with the other one.)

Done absolutely awesomely in Orson Scott Card's Pastwatch: The Redemption of Christopher Columbus. The plot is rather complicated, but suffice it to say it emerges that our own timeline is the product of interference from another timeline, in which the Tlaxcalans of Central America conquered Europe and possibly the world. (The author does an excellent job of making it sound plausible). The people of that timeline viewed the Tlaxcalan invasion as the greatest catastrophe in human history, and so they altered their own timeline, by motivating Christopher Columbus to sail west (with a holographic God). Of course, in the story our own timeline appears to be headed for human extinction, so the characters make their own alteration, preventing both the Central American and European civilisations from wiping each other out. They are apparently more successful than the original alterers.

This is because the protagonists have realized that the reason the original "interventionists" failed was because they made a single alteration and didn't see it through. Instead of sending a holo-recording, they decide to send three people with a plan for each. One's job is to destroy Columbus's ships and die in the process, preventing him from returning to Europe. Another, a native Mayan, has to unify the Central American peoples and teach them a milder version of Christianity. The third, an African female, has to teach Columbus the error of his ways and, along with him, unify and educate the peoples of the Caribbean islands in the same manner as her partner. The end result is that, when the ocean-going ships from the new American confederation arrive to Europe, they do so as equals. This prevents the world dominated by either the Europeans or the Native Americans. No direct explanation is given for the lack of an ecological catastrophe in this version of history.

Averted in Animorphs. When the kids travel back in time to stop Visser 4 from messing with history, they consider using the Time Matrix to change history for the better. However, they hit the Reset Button by accident and put everything back the way it was (minus one host body for Visser 4).

Although there was a sort of Merged Reality when Elfangor and Visser Three both activated the Time Matrix in The Andalite Chronicles.

Live Action Television

On Sliders, the Big Bad of the last season tried to do this, experimenting by first merging people from different universes together.

This is what essentially would have happened if Buffy hadn't stopped Glory in Buffy the Vampire Slayer. It would have been only temporary, though.

In Fringe, due to the activation of the Vacuum by Peter, a bridge is created between both the Prime and Alternate universe, preventing them from further collapse. This allows both universe's team to have the time to try and solve the problem.

Video Games

Inverted in the computer game The Longest Journey: the idea is to prevent the two worlds from combining, at least under the current uncontrolled conditions.

Similarly, the combining of the two worlds in the Super Mario Bros.Movie was a plot of the antagonists to rule them both.

Tales of Symphonia ends up with this being the goal of the main characters, although for much of the second half of the game they are under the mistaken impression that they need to do the exact opposite in order to Save Both Worlds. It just so happens that the resulting combination ends up being the world map of Tales of Phantasia.

It doesn't quite go as planned, as shown by the sequel/spinoff that came after. Only when Ratatosk (in the Good Ending) decides to rewrite the laws of nature so that life does not need mana to survive does everything ultimately work out.

In Tales of Eternia, the two main worlds begin colliding. The heroes only manage to fix it just in time by exploding the barrier between Inferia and Celestia, blasting the planets away from each other and altering the very nature of their universe. In the final scene, one of them is planning to upgrade their spaceship so they could go between worlds and visit their friends.

Tales of Innocence revolves around multiple factions looking to get their hands on a MacGuffin for different purposes. The main characters' is to unite Heaven and Earth into one paradise.

Subverted in Final Fantasy V, where this is exactly what Omnicidal Maniac Exdeath wants to happen and the heroes are trying to prevent. As it turns out, the power he's after was sealed by splitting the world in two hundreds of years ago, and he can only release it from the Dimensional Rift by reuniting the worlds (which entails the destruction of the Crystals, so with or without Exdeath actually claiming his prize and wreaking havoc with it, everybody's pretty much screwed). Double subverted when Exdeath succeeds in reuniting the worlds, so the heroes settle for protecting the merged world.

Exdeath: I will return the world to its original form! Bartz: To a world of evil! Exdeath: Are you even listening to me?

In Mortal Kombat vs. DC Universe, the Big Bad is Dark Kahn, a merged version of Shao Kahn and Darkseid, who starts merging the realities of Mortal Kombat and the DC Universe, while feeding off the rage of the characters. He's also playing the heroes and villains of each world against each other, which think that the other is an invading army. Eventually, though teamwork, Superman and Raiden manage to defeat Dark Kahn and split the merged universe back into two and Dark Kahn himself back into Darkseid and Shao Kahn... who end up in each other's world and therefore powerless. Darkseid gets confined into the Netherrealm, while Shao Kahn gets banished to the Phantom Zone.

In Eternal Darkness the true ending is obtained by playing the game three times, choosing a different Ancient as Pious' patron each time. In each path a different Ancient is slain. The true ending reveals that the entire game was Mantorok's plot to eliminate the three Ancients since he could no longer keep them in check thanks to Pious turning his own magic against him. The Tome of Eternal Darkness guided the player characters throughout history to kill a different Ancient in each timeline. Then Mantorok merged the three timelines so that all three of the Ancients were killed, leaving him and his own counterpart Ancient as the last of the Ancients.

Happens in the browser-based game no-one has to die.. Four normal endings, each with only one character left alive, each of them walk into a time machine, and meet up in a Merged Reality for the final ending.

Judge Dredd: Dredd vs. Death: When Judge Death retreats to his home dimension after his body is destroyed by Judge Dredd, he reveals to Dredd that his new plan is to use the Psi-Judges' energy to merge Deadworld with Dredd's universe, killing every living thing in Mega City One.

In Sonic Rush, Eggman's theft of the Sol Emeralds from Blaze's dimension is causing it and Sonic's dimension to merge together. Eggman and his doppelganger Eggman Nega plan to build a transdimensional Eggmanland in the wake of the collision, but the heroes are able to stop them before both worlds are completely ruined.

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